Comparative Genetic Mapping in Trees: The Group of Conifers

Abstract

The power of comparative genomics is widely accepted and applies to all taxa (Sankoff and Nadeau 2000). The genomes of the model systems Arabidopsis (The Arabidopsis Genome Initiative 2000) and rice (Goff et al. 2002; Yu et al. 2002) have been completely sequenced and are used to aid in positional cloning of genes from related species having much larger genomes and lacking a complete genome sequence. Comparative mapping among nonmodel species helps to understand the evolution of plant genomes (Bennetzen and Freeling 1993; Gale and Devos 1998) and can help validate quantitative trait loci (QTL) from one crop species to another (Paterson et al. 1995). Although there is no known small genome model species in conifers to be the equivalent of Arabidopsis and rice, conifers would still benefit significantly from an organized comparative mapping effort. Comparative mapping in plants began with the rather simple demonstration that maps in one species could be constructed using restriction fragment length polymorphism (RFLP) probes from a related species and once such maps were made, they could be compared (Bonierbale et al. 1988; Ann and Tanksley 1993). Loci revealed by RFLP probes are assumed to be orthologous between species, meaning that the gene was present in a common ancestor (Fig. 1). In contrast, paralogous loci result from duplications following speciation. Comparative maps have now been made for species in several important plant families including Brassicaceae (Paterson et al. 2000; Barnes 2002; Hall et al. 2002), Poaceae (Feuillet and Keller 2002; Laurie and Devos 2002; Ware et al. 2002; Ware and Stein 2003) and Solanaceae (Doganlar et al. 2002). The syntenic relationship among species provides insight into the type and number of chromosomal rearrangements that have occurred in the evolution of these plant groups. The international genome mapping community in forestry is very small and many different tree species are involved. For example, there are probably no more than 20 labs worldwide actively constructing forest tree genetic maps and there are at least an equal number of species being mapped. Forest